Alter
by Darksidejuggalo
Summary: First posted Fanfiction and very excited to show what I've got. An alternate story where the Uchiha are not wiped out and naruto does not live his life as a hidden leaf shinobi. Eventual Akatsuki Itachi and Naruto. Good Nagato. (apologies for the weak summary) Possible eventual M Current T
1. Chapter 1

Alter

Hey guys, this is my first fanfiction and as such any criticism (preferably constructive) is welcome and , lack of a proper flow, or a any lore issues I may commit. Also looking for a beta reader as I don't have Word and I'm hoping someone with a more professional client will be able to do some more professional editing that may or may not be done. On with the story eh?

So this is Alter (as an alternate to Naruto and its own blaring issues I'm sure I will have many of). In this story we will follow Naruto Uzamaki and Itachi Uchiha. No Slash! or any kind of male homosexual relationships (I have nothing against it I simply cannot write it as I constantly feel I'm being insulting or otherwise. I support all do you etc etc). Some ships I've already kind of set in stone others you guys have full input on! So comment on my dear readers. Now on with the story of Alter!

Itachi brought his blade down again, cutting down another member of his clan. He felt no pride, no shame, he felt empty. His eyes were hollow except for the blazing red of his sharingan. 'It had to be this way...to save the lives of many, few must die...'

His mind flashed back to the men who had given him this mission, Danzo and the third Hokage. "Itachi, are you sure you want to do this? There are still more...peaceful ways we can handle this. It still may be possible to achieve piece without bloodshed." Hiruzen said. Danzo sat next to him in the Hokages office, while Itachi was kneeled before them.

"Come Hiruzen, you know this cannot be! The Uchiha are one of the largest clans in Konoha! There is little we can do at this point. The Uchiha's coup will not wait forever and their numbers are growing. Only with the complete extermination can peace truly be achieved." Itachi flinched at the harsh sound of Danzo's words. 'Exterminate' rang through his mind over and over as he kneeled before them. There had to be another way. Danzo was right though, there is no way for peace to be achieved diplomatically, death will be wrought in some form. But must it be the whole clan?

Itachi was deep in thought for a time before a thought hit him. Many of the Uchiha will die- the leaders of the coup, those who held power inside the plan...his father. The Uchiha held little more than 1/16th of the villages total population, and even less trained shinobi. From what he could gather and what little intel a few other spies could gather, he would have to kill nearly 40 fully trained shinobi. All of which would have awakened their sharingan with atleast a half having fully awakened all three tomoe. Then there was the mangekyou. His father held one, and his right hand Daichi had his own. He wasn't sure how far Daichi had mastered his but he knew his father could even activate the susanoo as well as a unique power. What it was he wasn't sure but unless he wanted to have a full blown battle in the Uchiha compound he would have to kill his father before things escalated.

With all of this in mind Itachi rose and looked between the true leaders of the village hidden in the leaf. "I will not destroy my clan, nor will I doom them to extinction. I will instead hunt down and kill each of the heads of the coup as well as any supporters. Only those he stand against or know nothing about it will remain...this is the only way I will continue" Itachi looked between the two men, both of whom held looks of deep contemplation. Hiruzen spoke first "This...is better than I could've hoped, I will stand behind this decision but only if we're in agreement there is no possible way that this can be ended peacefully" Itachi and Danzo both shook their heads, with danzo standing "While it does not have the assurance that exterminating them all holds, I will stand behind it as well. Though I will be putting my own men in place after the act is done to assure that there is no chance at another coup being attempted." With this Danzo walked out of the room leaving Itachi alone with Hiruzen.

"Itachi...this is a hard path you have chosen. Are you sure you can go through with it? Once you start you cannot stop until the deed is done or my hands will be tied." Itachi sighed and nodded. "There is no other way, my clansman will not stand down, they feel as if they have been wronged and that it can only be rectified by blood. I will not have a civil war brew within our walls. By following my plan and leaving the rest alive, my people will live and be able to flourish again. Konoha will be there to support them in this time of despair and our bonds will be forged anew. It is the only way." Itachi's hands were shaking but he gave no reprieve. Hiruzen simply nodded. "Then you will be labeled a missing nin and given the label of a murderer. Never again will you be welcome within Konoha's walls or surrounded by the warmth of your kinsman. A bounty will be placed on your head as an S-class criminal. Anbu will be dispatched to hunt you down come sunrise. That is all I can offer you in return of your efforts. I'm sorry."Itachi for his part held his composure and nodded before disappearing in a cloud of smoke and an audible "Poof!"

Now he stood upon his final victim, the one he'd been dreading most. He stood in his own home in his parents bedroom. Covered in blood and eyes glowing he stared at his father, resting in bed. H'd been here for minutes now without doing anything. He couldn't do anything. It was his own father, the man who had raised and trained him, he couldn't kill him in cold blood...but he was also the leader of the coup who sought to lead Konoha into a bloody civil war. "It had to be this way...to save the lives of many, few must die."

He'd been repeating this to himself for hours now as he went from home to home murdering his clansman one by one. It was his crutch. Now, it was failing him. He couldn't stop now though, this was the pivotal moment. If Fugaku lived then the coup would rebuild through his words. He was the leader of the Coup and the head of the clan.

"It had to be this way...to save the lives of many, few must die."

Steeling himself he stepped forward, and then another. Soon he found himself standing in front of Fugaku with his blade raised. "I'm sorry...it had to be this way." But right as Itachi uttered these few words Fugaku flew from his bed, eyes flashing red as his sharingan spun to life. But it was too late, Itachi's blade swung down and cleaved his father through his shoulder before the blade dug deep into his chest. Itachi could just see his father's eye's spinning into a mangekyou sharingan before his eyes closed and he fell to the floor in front of Itachi. Itachi however had reverted into nothing more than a hollow. His body felt nothing and his mind was empty. Kneeling down he dug his fingers into his fathers eye socket and dug out his eye, still glowing with the power of his mangekyou. He pulled a small vial out and stored them inside.

Itachi knew the power of a fully awakened sharingan was coveted far and wide, their eyes often being the target of assassinations so that others could implant them in an attempt to gain their power. Who knows what those same people would do in the pursuit of a mangekyou sharingan- even if those who know about such an awakening could be counted on one hand. Storing them away in a small pouch next to Daichi's. He could hear his mother stirring and flew from the room, off into the night. He had previous little time to escape and he needed to make every second count lest he be forced to spill more blood.

And there we have it! Chapter one of Alter. I believe it's roughly a thousand words and while I could diffidently kept writing, I feel that this was a good stopping point and a thousand words is a good start. I like to think I'll be able to average four or five thousand words per chapter but I won't hold myself to any guidelines past a thousand words. A very important thing i forgot to touch on is that each character in this story are being aged up about sixteen years, I will attempt to keep this as lore friendly as possible but I find it very difficult to write children into a romantic situation and I won't be writing a time skip anytime soon. Itachi right now is roughly 27. Also as stipulation beta readers should hopefully adhere to these guidelines when applying.

-Good knowledge of grammar and word flow (I do not want to be one of those stories that are poorly written with a good story)

-deep understanding of Naruto lore and timelines (not too much of a necessity more of a want than a need)

-Flexible with time tables and are willing to actually set aside time to read and assist in editing these chapters. I will not have a post delayed by a beta reader.

-and to the one who gets the job, in case I don't say it enough. I will literally love you forever because I love writing and can't wait to get better with your assistance. Till next time, Darksidejuggalo out!


	2. Chapter 2

Alter chapter two

Naruto stumbled back to his apartment, his body barely holding his own weight. Villagers ignored his presence, but at this point he didn't really care. He felt nothing after yet another intense day of training- no gains in strength or speed. His ninjutsu was no better and the only thing gaining any headway was his taijutsu, but even that was marginal at best. He knew it was from a lack of proper instruction, nothing would get better if he simply continued with the few things he could pick up from books. But Kakashi spent all of his time training Sasuke, the prodigal son. Shino was being trained personally by his father, head of his clan and a master in their respective kekkei genkai. No one wanted to spend their time working with Naruto. Hell, he spent most of his time either training or hiding in his room lamenting over his failures.

He failed to pass the academy twice, failed to support almost at all on his team, and he failed to pass while Shino and Sasuke both became chunin. At this point he was debating giving up becoming a shinobi, what was the point? He'd never be good enough and he'd never be able to catch up with his classmates. Hell, the only time he saw any action was when the neighborhood bullies worked up the courage to pick a fight with him. Naruto may not be a powerful shinobi but he was more than able to deal with a few street thugs.

Sighing, Naruto turned the corner down an alley to his apartment when he heard someone call out to him. "Hey Naruto! Is that you?" Naruto turned and was surprised to see Mizuki sensei jogging towards him, a pleasant smile on his face. "Oh...Oh! Mizuki sensei! What's up?" Mizuki walked over to Naruto and clapped a hand on his shoulder, his smile only gaining strength. "Well I saw you and you seemed pretty down, so I thought I'd see what the problem was ya'know?" Naruto gaped at this, no one had ever been this nice to him. His brain actually shut down for a second as he tried to process what was being said to him- only coming back to his senses when Mizuki prodded him slightly. "Hey Naruto? You still in there?"

Naruto gulped and nodded. "Yea...yea sorry, I was just thinking. It's just...I can't seem to get anywhere in my training! Kakashi is too busy training Sasuke and Shino is being trained privately by his father. I've tried getting some books from the library but so much of it doesn't make any sense to me. I understand the basic concepts of ninjutsu and genjutsu but when it comes to the actual application of it I just can't get it right! The only thing that's gone anywhere is my taijutsu and even that is lousy compared to my teammates! I know I can be stronger if only I had the right teacher, but no one will train me. They're all to busy, which is fine I guess I can't expect them to put their life on hold just for me but it'd be nice if I could find someone to help me." Chuckling softly, but eventually turning into roaring laughter, Mizuki effectively broke down. Large gasping breaths filled the air as he attempted to collect himself enough to speak. "Jeez Naruto, do you pause when you talk? When I asked what was wrong I didn't expect it all at once!" He chuckled a few more times as Naruto visibly shrunk into himself. "Sor..sorry Mizuki sensei, I guess I'll just go home. Sorry for bothering you." Naruto went to turn around but Mizuki stopped him, waving his apologies off. "No no no! That's not what I meant at all Naruto! Listen, I'll be honest. I've noticed how hard you've been training by yourself. Anybody with determination like that definitely has potential. But you're right, you won't be getting anywhere without some proper instruction. So I went ahead and set up a test."

Naruto's eyes widened, was this his chance? "What's the test? I'll do it, whatever it is it doesn't matter!" Naruto was close to jumping for joy. He could do this! Mizuki smiled at Naruto's eagerness. "It's a rather well rounded test if I say so myself. It tests most if not all aspects of being a shinobi, so don't expect it to be easy alright?" Naruto nodded furiously, seemingly holding on by a thread.

"Alright so listen, right now it's around eight-thirty, you have until sunrise to break into the third hokage's office and found the scroll of seals. Once you find that you meet me in the woods just-" Mizuki pulled out a map and unrolled it with a flourish, "here. If you are detected you fail. If you kill anyone you fail, and if you take more than one scroll- you fail. Pass this test, and you'll receive training from a jounin level teacher." Naruto nodded but furrowed his brow as though in deep thought.

"But Mizuki sensei, who will be my teacher? As far as I know all available jounin are currently heading a squad of genin." Mizuki nodded at this, smiling all the while. "Correct Naruto, and as much as I would love to tell you, it's currently undecided. Lord Third is assessing a list as we speak, though I would think he has retired for the night. I have given you my highest recommendation." Mizuki looked to the sky, sighing slightly. "But Naruto, you don't want to waste time- breaking into a Kazekage's office is no small feat." Naruto nodded and dashed off, leaving a faint cloud of dust as he hurried to his goal.

Mizuki smiled in an almost feral way. 'I wasn't lying when I said that boy was determined, his skill is well into the chunin category even if he doesn't realize it himself. Comparing himself to greats such as Shino or Sasuke. Regardless though, once he gets me that scroll, I'll kill him and return to Orochimaru. Then I will have my curse mark finished!' Mizuki chuckled to himself before disappearing in a cloud of smoke.

- _Hokage's Residence-_

Naruto grunted as he landed within the Hokage's office, having just dodged a patrol that had been turning the corner. Sighing he stood and dusted himself off. 'Hm...getting into the office was easier than I thought, after this I may want to tell the Hokage his security sucks..' Naruto thought, before shrugging his shoulders and looking around the office. He didn't see any scrolls but he also didn't expect to. Running his hands along the walls while also softly knocking. He had gone around three walls before hearing a hollow sound coming from the fourth, to the right of the door. "Hehehehe...this is almost too easy." Searching around slightly Naruto found a small loose tile and lifted it, triggering a lever and causing a soft ' _pop'_ to be heard. Looking up Naruto saw a panel in the door had popped out and upon pushing it further, found a rack of large scrolls. Naruto panicked slightly, as for a moment they all looked the same, but upon closer inspection he saw a small label under each scroll on the rack. Naruto grinned and almost whooped for joy. 'This is it! I'll finally become a true shinobi!' Quickly grabbing the scroll and strapping it to his back, Naruto unlocked the window barring his exit and climbed out...dashing onward to his future...

 _Hey there! Sorry for the crap update time but things are going on in life. Moving states and starting school a few weeks short as well as figuring out a number of legal matters. I do hope I haven't let anyone down and I promise, I am not giving a one and done story that flood much of this site. Until next time, DarksideJuggalo_


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